3.1 Effect of ROS quenching on cyanobacterial cell growth in co-culture system
With the potential to react with biomolecules including nucleic acids, proteins and lipids, ROS can cause oxidative stress to cells, leading to cellular damage 32. Previous studies pointed to the possibility that heterotrophic bacteria can remove ROS in medium to improve cell growth of cyanobacteria in co-culture system, eventually enhancing the stability of co-culture system 13, 14. To verify this hypothesis, ascorbic acid was added into CoBG-11 medium to decrease ROS generation through directly scavenge O2•‐, •OH and reduce H2O2 to water 33. Different concentrations of ascorbic acid, 0.1 mM, 1 mM, 2 mM were added into pure cultural SynechococcuscscB+ respectively in CoBG-11 34, 35, the analysis showed that SynechococcuscscB+ grew better with additional 1 mM ascorbic acid in CoBG-11 compared with 0.1 mM ascorbic acid supplementation, while cell growth was inhibited after three days when supplemented 2 mM ascorbic acid (Fig. 1A). Consistently, the analysis showed that H2O2 content was significantly decreased with ascorbic acid added (Fig. 1B); however, it is unclear why the cells growth was arrested when 2 mM supplementary ascorbic acid led to almost no detectable H2O2 at 4 days. More importantly, although cyanobacterial growth was obviously improved with additional 1 mM ascorbic acid under pure culture, cyanobacterial growth was still slower than that in co-culture with E. coli, suggesting that the better growth of SynechococcuscscB+ might be caused by other factors more than just ROS quenching.
3.2 Analysis of key metabolites in S. elongateus cscB+ during co-cultivation by target LC-MS metabolomics
As the stability and productivity in the co-culture system was dependent on the cyanobacterial sucrose production, intracellular levels of key metabolites within Synechococcus cscB+ cells were investigated. LC-MS based metabolomics approach, which has been employed previously to comparatively analyze cellular metabolism in the engineered cyanobacterial strains 29, 36, was applied to compare co-cultivated and pure cultural Synechococcus cscB+. As shown in Fig. 2, twenty-one metabolites of cyanobacterial metabolism involve in glycolysis, amino acid, and the citric acid (TCA) cycle were chemically classified. Comparative analysis showed that the intracellular contents of FBP, F6P, E4P, R5P and acetyl-CoA were increased, suggesting more carbon sources were utilized in co-cultivated Synechococcus cscB+. Five amino acids, lysine (Lys), serine (Ser), valine (Val), alanine (Ala) and phenylalanine (Phe) were found with significant up-regulation during co-cultivation condition. Three metabolites involved in TCA cycle including citric, malate and succinate, were also showed significant increases in co-cultivation condition. One possible explanation for the increased metabolites in glycolysis, amino acid, and TCA cycle is that increasingly available CO2, possibly from the respiration of heterotrophic cells, contributes to cyanobacterial better cell growth during co-cultivation, consistent with a previous finding that enhanced CO2 fixation and oil production in co-culturing green algal Chlorella and yeast Saccharomyces cerevisiae system 37. The results were also consistent with a more recent study which found salt stress redirect the fixed CO2 toward sucrose production rather than biomass and glycogen accumulation in engineered Synechococcus 2973 38. In addition, the results of LC-MS also implicated that the enhanced CO2 fixation could be used as an engineering target for further improving sucrose production in the co-cultivated cyanobacteria by modulating sucrose production pathway.
3.3 Analysis of cyanobacterial metabolic responses to E. coliin co-cultivated S. elongateusby transcriptomics
For the interaction based on cross-feeding and metabolite exchange, early studies have shown that heterotrophic bacteria could also be involved in providing essential micronutrients, such vitamins, amino acids and bioavailable trace metals, necessary to maintain high photosynthetic productivity 39. To explore the mechanism underlaid the increased cell growth of co-cultivated cyanobacteria, and to determine the factors necessary for the stability and fermentation performance, transcriptomics between pure cultural cyanobacteria (C) and co-cultural cyanobacteria with E. coli (D) was applied to analyze the interaction mechanism of cyanobacteria responses to the heterotrophic partner in co-culture system. With a cutoff of 1.5-fold change and a p value of statistical significance less than 0.05, we found 120 genes up-regulated and 104 genes down-regulated as a result of co-cultivation, respectively. The reliability and accuracy of the transcriptomics data was independently verified by real-time quantitative PCR (qRT-PCR) (Suppl Table S1), the correlation coefficient R2 was 0.9086 (Fig. S1), indicating the transcriptomics data collected in this study is of very high accuracy. The analysis showed that a large fraction of up-regulated transcripts was affiliated with photosynthesis and oxidative phosphorylation (25%), signal transduction and membrane transport (13%), translation (10%), genetic information processing (6%), metabolism of cofactors and vitamins (3%) role categories (Fig. 3A, Suppl Table S2), suggesting the key central metabolism of cyanobacterial cells was affected by the presence of E. coli in the co-culture system.
The analysis showed significant increases in transcripts levels of phosphate transport system permease genes M744_04015 (pstS, sphX), and M744_04030 (pstA), and iron transporter (for example, bicarbonate transporter M744_01215, calcium/sodium antiporter M744_01815, P-type Cu2+ transporter M744_04705), suggesting higher availability of these important micronutrients for Synechococcus cscB+ during co-cultivation condition 40. Meanwhile, the gene M744_08450 (cmpD encoding a bicarbonate transporter) was significantly down-regulated, which illuminated that CO2 availability might be increased due to the fact that E. coli ABKm might provide additional CO2 for co-cultivated Synechococcus cscB+. In addition, M744_08660 (modA) encoding a molybdate transport system substrate-binding protein was also found down-regulated. Molybdenum is an essential component of the cofactors of many metalloenzymes including nitrate reductase and Mo-nitrogenase 41, the down-regulation of modA might suggest that more nitrogen available for Synechococcus cscB+ during co-cultivation as well. Varkey et al. described the up-regulation in several translational, ribosomal biogenesis and transcriptional proteins under oxidative stress in marine Synechococcus isolates 42. However, many transcripts involved in ribosomal proteins (M744_13675, M744_13670, M744_05205, M744_00735, M744_05210, M744_12320, M744_05195, M744_05180, M744_05185), tRNA synthetases (M744_03935, M744_5340) and RNA binding protein (M744_12800) were down-regulated in our study, which likely due to the reduced ROS content in co-culture system 13. The down-regulated transcripts in co-cultivated Synechococcus cscB+ compared with under axenic condition were also demonstrated (Suppl Table S3).
Consistent with abovementioned results, significant decreases in transcripts levels of oxidative stress related genes were found in co-cultivated Synechococcus cscB+, including two genes (M744_11065 and M744_01810) encoding high light-inducible proteins (Hli), M744_03995 encoding antioxidant protein and M744_07160 encoding heme oxygenase, indicating possible reduced oxidative stress in co-cultivated Synechococcus cscB+. High light-induced proteins are critical for the energy dissipation mechanism to resist oxidative stress in cyanobacteria 43. He et al. found the gene expression of 4 hlis genes were induced under low temperature, strong light stress and nutrient deficiency condition in Synechocystis sp. PCC 6803 (hereafter as Synechocystis 6803), and the hli knockout mutant strain could not be survival under strong light, suggesting that the high light-induced protein may play a photoprotective role 44. The ferredoxin-dependent heme oxygenase catalyzes the degradation of heme to produce biliverdin IXα with the release of ferrous iron 45. Cheng et al. found the down-regulation of heme oxygenase gene might reduce the release of detrimental free iron that causes oxidative stress 46. Consistent with these results, our finding that the down-regulation of these four genes that the better growth of Synechococcus cscB+ in co-culture system was partially attributed to the quenching of ROS by heterotrophic partner E. coli ABKm. In a previous study, Vance et al. found that the phospholipid/cholesterol/gamma-HCH transport system permease protein (MlaE) was down-regulated after exposure to a high bisphenol A concentration, which might inhibit phospholipid transport, and subsequently altered the spontaneous diffusion of the membrane to eventually caused membrane damage 47. Interestingly, the relative expression of M744_01095 (mlaE) was also increased in co-cultivated Synechococcus cscB+, which also suggested that ROS induced membrane damage was relieved by the presence of the heterotrophic partner.
In cyanobacteria, the secretory (Sec) pathway is critical for proteins transportation across the plasma membrane and thylakoid membrane 48. The core of translocase in Sec pathway is a protein channel assembled by heterotrimeric membrane protein complex SecYEG and ATPase SecA oligomers, SecA is used as a molecular motor 49. It was estimated that 82% of translocated proteins in Synechocystis 6803 contain a Sec signal peptide 50. The expression of M744_13645 (secE) was up-regulated in co-cultivated Synechococcus cscB+. In addition, the relative expression of M744_09155 (yidC) was increased in co-cultivated Synechococcus cscB+ as YidC protein mediates integration of membrane integral proteins in bacteria and thylakoid membrane 51. The increased expression levels of secE and yidC were consisted with the phenotype of better cyanobacterial growth as translocase is responsible for the insertion of the photosystem integral membrane proteins into the thylakoid membrane in cyanobacteria 52.
3.4 Analysis of cyanobacterial metabolic responses to E. coliin co-cultivated S. elongateusby quantitative proteomics
The low correlation between mRNA and protein expression has been found and well discussed in previous studies, which might be caused by the widespread post-transcriptional regulation mechanism53, 54. For example, Nie et al. found that correlation of mRNA expression and protein abundance was affected at a fairly significant level by multiple factors related to translational efficiency 55. In order to fully identify the interaction mechanism in the co-culture system, the quantitative iTRAQ proteomics was used to analyze cell responses of Synechococcus cscB+ adapt to E. coli in co-culture system. Three Synechococcus cscB+ samples from the co-culture (E1, E2, E3) and three from the axenic culture (C1, C2, C3) were collected after cultivation of 96 h, respectively, and the differential profiles of proteins in Synechococcus cscB+ were identified by setting comparison groups of E1 vs. C1, E1 vs. C2, E1 vs. C3, E2 vs. C1, E2 vs. C2, E2 vs. C3, E3 vs. C1, E3 vs. C2, E3 vs. C3. The proteomic analysis identified a total of 914,635 spectra, among which 21,603 unique spectra met the 1% FDR filter and were matched to 2,206 unique proteins in the genome. In addition, a good coverage was obtained for a wide MW range for protein (Fig. 4A). Most of the identified proteins were with good peptide coverage, ~89% of the proteins were with more than 10% of the sequence coverage and ~87% were with more than 20% of the sequence coverage (Fig. 4B). Among the functional categories, the “general function prediction only” was the top detected functional category, representing 13.43% of all the identified protein (Fig. 4C). This result is consisted with the previous finding that approximately 45% of proteins in the cyanobacterial genome are hypothetical proteins 56. Other frequently detected functional categories included “translation, ribosome structure and biogenesis” (9.42%), “amino acid transport and metabolism” (8.67%), “posttranslational modification, protein turnover, chaperones” (8.51%), “signal transduction mechanism” (7.17%), “carbohydrate transport and metabolism” (6.51%).
All 251 differentially expressed proteins were divided into 21 secondary branches of pathways based on the KEGG database classification, in which 181 differentially regulated proteins are related to cell metabolism, including energy metabolism (10.36%), metabolism of cofactors and vitamins (10.36%), carbohydrate metabolism (10.36%), and amino acid metabolism (4.38%) (Fig. 5A). The number of up- and down-regulated proteins in each annotated pathway was shown in Fig. 5B. The KEGG enrichment analysis suggested that seven pathways were significantly enriched (P-value<0.05) in the up-regulated differential proteins, including “two-component system”, “nitrogen metabolism”, “biofilm formation-E. coli”, “lipoic acid metabolism”, “sulfur relay system”, “ABC transporters”, “glyoxylate and dicarboxylate metabolism” (Fig. 5C), while only “ABC transporters” was significantly enriched (P-value<0.05) in the down-regulated differential proteins (Fig. 5D).
3.5 Cyanobacteria responses to co-culture systemdeciphered by proteomics
As demonstrated in the transcriptomics analysis that the large fraction (25%) of transcripts involved in photosynthesis and oxidative phosphorylation were significantly increased during co-cultivation, the differentially expressed proteins involved in the energy metabolism pathway was also identified (Suppl Table S4). In co-cultivated Synechococcus cscB+, the increase of protein abundances for energy metabolism enzymes, such as ferredoxin (PetF, M744_01325), phycobiliproteins terminal rod linker (CpcD, M744_11425), photosystem II reaction center H (PsbH, M744_01910), photosystem II D1 protein (PsbA, M744_00850), NAD(P)H-quinone oxidoreductase subunit 4 (NadhD, M744_05920), and NAD(P)H-quinone oxidoreductase subunit 5 (NadhF, M744_01470) were observed, suggesting that more NADPH and ATP generated from photosynthesis 57, which is likely due to the elevated C and/or N availability compared with the axenic control, as discussed above. Meanwhile, increased protein abundance of the light-independent prochlorophyll reductase subunit B (ChlB) (M744_07280), which catalyzes the conversion of prochlorophyll to chlorophyll a 58, was also found, suggesting that cyanobacterial photosynthesis might be improved during the co-cultivation. These results are well consistent with our findings based on the transcriptomics analysis.
Nitrogen metabolism, either from nitrate or ammonium, governs the turnovers of the macromolecules that regulate metabolic pathways, eventually affecting energy production and carbon skeleton 59. Through the quantitative proteomics analysis, three nitrate/nitrite transport system ATP-binding proteins of M744_10450 (NrtB), M744_10455 (NrtC), and M744_10460 (NrtD) and two ferredoxin-nitrite reductases (M744_10440 and M744_07195) were found up-regulated in the co-cultivated Synechococcus cscB+, suggesting that the nitrite uptake in co-cultivated Synechococcus cscB+ was enhanced. The ammonium is incorporated into carbon skeletons through glutamine synthetase (M744_02210), which was also found up-regulated in co-cultivated Synechococcus cscB+. Significant up-regulation in the nitrogen uptake and assimilation were evident with higher photosynthesis and better cyanobacterial growth during the co-cultivation condition.
Phosphorus is a vital nutrient for cyanobacterial growth, which impacts the synthesis of cyanobacterial extracellular polymeric substances and also appears to induce significant changes in the synthesis of polysaccharides, as well as membrane lipids 60. In the co-cultivated Synechococcus cscB+, the proteins involved in phosphate transport system, including M744_04030 (PstA), M744_04035 (PstB), M744_04025 (PstC), M744_04020 (PstS) and M744_04015 (SphX), were found up-regulated by 2.08-, 2.12-, 3.80-, 2.67- and 4.75-fold, respectively. The up-regulation of all four phosphate transporters in the co-cultivated Synechococcus cscB+ might be due to the increased consumption of Pi in the form of NAPDH or ATP, which contributes to further cell growth. Consistently, the increased transcripts level of M744_04015 (sphX) and M744_04030 (pstA), were also found at transcription level. Aside from dissolved inorganic phosphorus, dissolved organic phosphorus is used by cyanobacteria via alkaline phosphatase 60. Two alkaline phosphatases (M744_09635 and M744_11635) in the co-cultivated Synechococcus cscB+ were found up-regulated by 2.89- and 1.40- fold, respectively, suggesting that the cyanobacteria were able to acquire more phosphorus for cell growth during the co-cultivation condition 40.
Two up-regulated proteins M744_05990 and M744_04340 annotated respectively as xylose-5-phosphate/fructose 6-phosphate phosphotransketolase (Xfp) and pyruvate-ferredoxin/flavodoxin oxidoreductase (Por), were identified in the co-cultivated Synechococcus cscB+. Xfp plays a key role in glycolysis, catalyzing the conversion of X5P or F6P to acetyl phosphate 61, while Por is responsible for the oxidation process of pyruvate to generate acetyl-CoA 62. The up-regulation of Xfp and Por indicated CO2 fixation might be enhanced in the co-cultivated Synechococcus cscB+, well-consistent with the increased acetyl-CoA content in the metabolomic analysis discussed above. In addition, three bicarbonate transporters, including M744_08440 (CmpB), M744_08445 (CmpC), and M744_08450 (CmpD) were also found down-regulated in the quantitative proteomics data, also consistent with the transcriptomic analysis. The cmp operon (cmpA, cmpB, cmpC, cmpD) in Synechococcus 7942 has been confirmed to encode a component of the ABC-type HCO3- transporter BCT1, and its transcription was activated at low CO2 concentrations 63, 64. The down-regulation of these three bicarbonate transporters indicated that the concentration of CO2 in the co-culture system might be higher than that under pure culture conditions, due to the fact that E. coli ABKm might secret CO2 to the system, which was also found in transcriptomics.
The exchange of essential micronutrients, such as vitamins, amino acids and bioavailable trace metal, from heterotrophic bacteria to cyanobacteria during co-cultivation was observed above at the transcript level. Pathway enrichment analysis of the proteomic data indicated that Synechococcus cscB+ had maximized the uptake and utilization of Fe3+ and thiamine to improve cell growth during the co-cultivation condition. Significant decrease in protein abundances of Fe3+ transporter, including AfuA (M744_05470) and AfuB (M744_09555) 65, indicated increased availability of this important micronutrient for S. elongateus cscB+ during the co-cultivation condition. The up-regulation of thiamine metabolism proteins was also found in the co-culture system. The cysteine desulfurase (M744_03415) catalyzes the conversion of L-cysteine to L-alanine and sulfur, the released sulfur was then transferred into scaffold protein to assemble Fe-S clusters 66, while the Fe-S clusters participate in electron transfer, iron-sulfur storage, regulation of gene expression, photosynthesis, and enzyme activity in all kingdoms of life 67. The up-regulation of M744_03415 was observed, consistent with the cyanobacterial growth and functional performance during co-cultivation. Thiamine pyrophosphate (TPP) acts as a cofactor for several enzymes in key cellular metabolic pathways such as glycolysis, the pentose phosphate pathway and the citric acid cycle (TCA) 68. Proteomic analysis showed that the phosphomethylpyrimidine synthase (ThiC) (M744_11180), an essential enzyme for TPP biosynthesis, was up-regulated in the co-cultivated Synechococcus cscB+, suggesting that enhanced carbon metabolic activity in Synechococcus cscB+. In addition, up-regulation was also observed for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (MenD) (M744_09410), which is involved in the biosynthesis of menaquinone and phylloquinone. Menaquinones play important roles in electron transport and oxidative phosphorylation, while phyloquinone is the secondary electron carrier in the photosystem I 69, their up-regulation was in general consisted with the improved growth of Synechococcus cscB+.
Moreover, the down-regulation of five proteins related to oxidative stress, including Hli protein (M744_01810 and M744_11065), fur family transcription regulator (Fur) (M744_05500 and M744_12665), and monothiol glutaredoxin (M744_10930) were found in the co-cultivated Synechococcus cscB+ by our quantitative proteomics analysis. The two Hli proteins were also identified in transcriptomic analysis. The transcription regulator Fur, as an iron uptake regulator, is responsible for controlling the gene expression of siderophore biosynthesis and iron transport 70. In previous studies, monothiol glutaredoxin was proved to protect against oxidative stress by regulating iron homeostasis 71. The crosstalk between controlling iron homeostasis and defending against ROS was previously confirmed in E. coli, demonstrating that the lack of iron regulation may lead to oxidative stress 72. Thus, the down-regulation of these five proteins indicated the positive effect on cell growth during the co-cultivation was attributed to the decrease of oxidative stress in Synechococcus cscB+ by a heterotrophic cells capable of ROS scavenging, which was also consistent with the our previous finding that the gene expression of three types of catalases, including hydroperoxidase I (katG), hydroperoxidase II (katF), and hydroperoxidase III (katE) were significant induced in E.coli during the co-cultivation condition 21.